Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

LHFP (lipoma HMGIC fusion partner)

Written2005-01Marleen Petit
Laboratory for Molecular Oncology, Department of Human Genetics, University of Leuven (K.U.Leuven) & VIB, Herestraat 49, B-3000 Leuven, Belgium

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)MGC22429
Other alias
HGNC (Hugo) LHFP
LocusID (NCBI) 10186
Atlas_Id 248
Location 13q13.3  [Link to chromosome band 13q13]
Location_base_pair Starts at 39342892 and ends at 39603219 bp from pter ( according to hg19-Feb_2009)  [Mapping LHFP.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

DNA/RNA

Description Exon-intron structure not described.
Transcription mRNA: ubiquitously: 2.4 kb; The ATG start codon is immediately preceded by an in-frame stop codon, and matches the most important positions of the Kozak consensus sequence; the 3'-UTR contains a CA-repeat.
Pseudogene No pseudogenes according to pseudogene.org.

Protein

  200 amino acids.
Description Database searches with the predicted LHFP amino acid sequences revealed no significant similarity to any known gene or protein or any known protein motif.
Expression Not known.
Localisation Not known.
Function Not known.
Homology LHFP is a member of a family of proteins, which contains 6 members: LHFP, LHFPL1, LHFPL2, LHFPL3, LHFPL4, LHFPL5.

Mutations

Somatic HMGA2/LHFP fusion gene encoding the three DNA-binding domains of HMGA2 followed by 69 amino acids encoded by frame-shifted LHFP sequences.

Implicated in

Note
  
Entity Solitary lipomas.
Disease Benign tumors of adipose tissue
Prognosis Can be surgically removed with no recurrence in most cases.
Cytogenetics More than 60% of solitary lipomas have an aberrant karyotype: 2/3 of these carry 12q15 rearrangements, most often translocations, affecting the HMGA2 gene:
  • 1/4 of the latter have chromosomal region 3q27-q28 (containing LPP) as 12q15 translocation partner (creating a HMGA2/LPP fusion gene).
  • In the 3/4 others, multiple chromosomes have been found as translocation partner of 12q15, one of these being chromosomal region 13q12 (containing, amongst others, the LHFP gene).
  • Hybrid/Mutated Gene HMGA2/LHFP hybrid gene containing the first three exons of HMGA2, which are followed by exon(s) of LHFP; under the regulation of the HMGA2 promoter.
    Abnormal Protein No known LHFP fusion protein. (HMGA2/LHFP fusion transcripts encode the three DNA-binding domains of HMGA2 followed by 69 amino acids encoded by frame-shifted LHFP sequences).
      

    Bibliography

    Clustering of deletions on chromosome 13 in benign and low-malignant lipomatous tumors.
    Dahlén A, Debiec-Rychter M, Pedeutour F, Domanski HA, Höglund M, Bauer HC, Rydholm A, Sciot R, Mandahl N, Mertens F
    International journal of cancer. Journal international du cancer. 2003 ; 103 (5) : 616-623.
    PMID 12494468
     
    LHFP, a novel translocation partner gene of HMGIC in a lipoma, is a member of a new family of LHFP-like genes.
    Petit MM, Schoenmakers EF, Huysmans C, Geurts JM, Mandahl N, Van de Ven WJ
    Genomics. 1999 ; 57 (3) : 438-441.
    PMID 10329012
     
    Absence of HMGIC-LHFP fusion in pulmonary chondroid hamartomas with aberrations involving chromosomal regions 12q13 through 15 and 13q12 through q14.
    Rogalla P, Lemke I, Bullerdiek J
    Cancer genetics and cytogenetics. 2002 ; 133 (1) : 90-93.
    PMID 11890997
     

    Citation

    This paper should be referenced as such :
    Petit, MM
    LHFP (lipoma HMGIC fusion partner)
    Atlas Genet Cytogenet Oncol Haematol. 2005;9(1):17-18.
    Free journal version : [ pdf ]   [ DOI ]
    On line version : http://AtlasGeneticsOncology.org/Genes/LHFPID248ch13q12.html


    Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 3 ]
      Soft Tissues: Lipoma / benign lipomatous tumors
    Soft Tissues: Ordinary lipoma with t(1;12)(p32;q14) HMGA2/PPAP2B
    Soft tissue tumors: an overview


    External links

    Nomenclature
    HGNC (Hugo)LHFP   6586
    Cards
    AtlasLHFPID248ch13q12
    Entrez_Gene (NCBI)LHFP  10186  lipoma HMGIC fusion partner
    Aliases
    GeneCards (Weizmann)LHFP
    Ensembl hg19 (Hinxton)ENSG00000183722 [Gene_View]
    Ensembl hg38 (Hinxton)ENSG00000183722 [Gene_View]  chr13:39342892-39603219 [Contig_View]  LHFP [Vega]
    ICGC DataPortalENSG00000183722
    TCGA cBioPortalLHFP
    AceView (NCBI)LHFP
    Genatlas (Paris)LHFP
    WikiGenes10186
    SOURCE (Princeton)LHFP
    Genetics Home Reference (NIH)LHFP
    Genomic and cartography
    GoldenPath hg38 (UCSC)LHFP  -     chr13:39342892-39603219 -  13q13.3-q14.11   [Description]    (hg38-Dec_2013)
    GoldenPath hg19 (UCSC)LHFP  -     13q13.3-q14.11   [Description]    (hg19-Feb_2009)
    EnsemblLHFP - 13q13.3-q14.11 [CytoView hg19]  LHFP - 13q13.3-q14.11 [CytoView hg38]
    Mapping of homologs : NCBILHFP [Mapview hg19]  LHFP [Mapview hg38]
    OMIM606710   
    Gene and transcription
    Genbank (Entrez)AF098807 AK129819 AK223369 AK313036 AL137388
    RefSeq transcript (Entrez)NM_005780
    RefSeq genomic (Entrez)
    Consensus coding sequences : CCDS (NCBI)LHFP
    Cluster EST : UnigeneHs.507798 [ NCBI ]
    CGAP (NCI)Hs.507798
    Alternative Splicing GalleryENSG00000183722
    Gene ExpressionLHFP [ NCBI-GEO ]   LHFP [ EBI - ARRAY_EXPRESS ]   LHFP [ SEEK ]   LHFP [ MEM ]
    Gene Expression Viewer (FireBrowse)LHFP [ Firebrowse - Broad ]
    SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
    GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
    BioGPS (Tissue expression)10186
    GTEX Portal (Tissue expression)LHFP
    Human Protein AtlasENSG00000183722-LHFP [pathology]   [cell]   [tissue]
    Protein : pattern, domain, 3D structure
    UniProt/SwissProtQ9Y693   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
    NextProtQ9Y693  [Sequence]  [Exons]  [Medical]  [Publications]
    With graphics : InterProQ9Y693
    Splice isoforms : SwissVarQ9Y693
    PhosPhoSitePlusQ9Y693
    Domains : Interpro (EBI)Lipome_HGMIC_fus_partner-like   
    Domain families : Pfam (Sanger)L_HMGIC_fpl (PF10242)   
    Domain families : Pfam (NCBI)pfam10242   
    Conserved Domain (NCBI)LHFP
    DMDM Disease mutations10186
    Blocks (Seattle)LHFP
    SuperfamilyQ9Y693
    Human Protein Atlas [tissue]ENSG00000183722-LHFP [tissue]
    Peptide AtlasQ9Y693
    HPRD09464
    IPIIPI00785082   
    Protein Interaction databases
    DIP (DOE-UCLA)Q9Y693
    IntAct (EBI)Q9Y693
    FunCoupENSG00000183722
    BioGRIDLHFP
    STRING (EMBL)LHFP
    ZODIACLHFP
    Ontologies - Pathways
    QuickGOQ9Y693
    Ontology : AmiGODNA binding  integral component of membrane  
    Ontology : EGO-EBIDNA binding  integral component of membrane  
    NDEx NetworkLHFP
    Atlas of Cancer Signalling NetworkLHFP
    Wikipedia pathwaysLHFP
    Orthology - Evolution
    OrthoDB10186
    GeneTree (enSembl)ENSG00000183722
    Phylogenetic Trees/Animal Genes : TreeFamLHFP
    HOVERGENQ9Y693
    HOGENOMQ9Y693
    Homologs : HomoloGeneLHFP
    Homology/Alignments : Family Browser (UCSC)LHFP
    Gene fusions - Rearrangements
    Fusion : MitelmanCOG6/LHFP [13q14.11/13q13.3]  [t(13;13)(q13;q14)]  
    Fusion : MitelmanHMGA2/LHFP [12q14.3/13q13.3]  [t(12;13)(q14;q13)]  
    Fusion : MitelmanTDRD3/LHFP [13q21.2/13q13.3]  [t(13;13)(q13;q21)]  
    Fusion : MitelmanUNC79/LHFP [14q32.12/13q13.3]  [t(13;14)(q13;q32)]  
    Fusion : COSMICHMGA2 [12q14.3]  -  LHFP [13q13.3]  [fusion_976]  [fusion_977]  
    Fusion: TCGACOG6 13q14.11 LHFP 13q13.3 BRCA
    Fusion: TCGAKIAA1409 LHFP 13q13.3 KIRC
    Fusion: TCGATDRD3 13q21.2 LHFP 13q13.3 BRCA
    Polymorphisms : SNP and Copy number variants
    NCBI Variation ViewerLHFP [hg38]
    dbSNP Single Nucleotide Polymorphism (NCBI)LHFP
    dbVarLHFP
    ClinVarLHFP
    1000_GenomesLHFP 
    Exome Variant ServerLHFP
    ExAC (Exome Aggregation Consortium)ENSG00000183722
    GNOMAD BrowserENSG00000183722
    Genetic variants : HAPMAP10186
    Genomic Variants (DGV)LHFP [DGVbeta]
    DECIPHERLHFP [patients]   [syndromes]   [variants]   [genes]  
    CONAN: Copy Number AnalysisLHFP 
    Mutations
    ICGC Data PortalLHFP 
    TCGA Data PortalLHFP 
    Broad Tumor PortalLHFP
    OASIS PortalLHFP [ Somatic mutations - Copy number]
    Cancer Gene: CensusLHFP 
    Somatic Mutations in Cancer : COSMICLHFP  [overview]  [genome browser]  [tissue]  [distribution]  
    Mutations and Diseases : HGMDLHFP
    LOVD (Leiden Open Variation Database)Whole genome datasets
    LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
    BioMutasearch LHFP
    DgiDB (Drug Gene Interaction Database)LHFP
    DoCM (Curated mutations)LHFP (select the gene name)
    CIViC (Clinical Interpretations of Variants in Cancer)LHFP (select a term)
    intoGenLHFP
    NCG5 (London)LHFP
    Cancer3DLHFP(select the gene name)
    Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
    Diseases
    OMIM606710   
    Orphanet
    MedgenLHFP
    Genetic Testing Registry LHFP
    NextProtQ9Y693 [Medical]
    TSGene10186
    GENETestsLHFP
    Target ValidationLHFP
    Huge Navigator LHFP [HugePedia]
    snp3D : Map Gene to Disease10186
    BioCentury BCIQLHFP
    ClinGenLHFP
    Clinical trials, drugs, therapy
    Chemical/Protein Interactions : CTD10186
    Chemical/Pharm GKB GenePA30358
    Clinical trialLHFP
    Miscellaneous
    canSAR (ICR)LHFP (select the gene name)
    Probes
    Litterature
    PubMed10 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    CoreMineLHFP
    EVEXLHFP
    GoPubMedLHFP
    iHOPLHFP
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

    Search in all EBI   NCBI

    © Atlas of Genetics and Cytogenetics in Oncology and Haematology
    indexed on : Thu Oct 12 16:25:55 CEST 2017

    Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

    For comments and suggestions or contributions, please contact us

    jlhuret@AtlasGeneticsOncology.org.